The jury in the trial of Independent TD Michael Lowry has been told an alleged missing invoice is "no conjuring act" and there is "an innocent explanation" for the missing document.

It is the State's case Mr Lowry's company, Garuda Ltd, received stg£248,624 in commission from Norpe OY, a refrigeration company based in Finland, in August 2002. It is alleged Mr Lowry arranged for this payment to be made to a third party, Kevin Phelan, residing in the Isle of Man, and therefore it didn't appear in the company accounts for that year.

It is further alleged the accounts were then falsified in 2007 to reflect that the payment was received in 2006.

Patrick Treacy SC, defending Garuda, reminded the jury the politician's secretary, Aileen Dempsey, gave an explanation for the reason there was no invoice for the money. He said Norpe told her an invoice had to come from Mr Phelan directly rather than Garuda and that was the "innocent explanation". "It is no conjuring act," Mr Treacy said. He said it was "a key moment in the trial" yesterday when a charge against Mr Lowry of making an incorrect income tax return was dropped. He said that charge existed because a tax inspector determined the stg£248,624 was an emolument (a wage or salary), and because of that both Mr Lowry and Garuda owed income tax, PAYE and PRSI.

They were assessed as owing a total bill of €1.1m including interest, fines and penalties. This assessment was later successfully challenged before the appeals commission. "That was the engine driving this whole case. The engine ran into a serious problem in terms of staying on track." He said when this charge against Mr Lowry was dropped, the prosecution "went up with a puff of smoke".

Referring to the opening speech of prosecution counsel Remy Farrell SC, who said Garuda's books were "cooked, not once but twice", Mr Treacy said "the only cooking being done now is by Revenue and they have overcooked the books".

He asked the jurors to ask themselves a "fundamental question" if it is right his client should be prosecuted in Dublin Circuit Criminal Court by Revenue in relation to an underpayment of corporation tax of €5,541.

Yesterday, Judge Martin Nolan told the jury a charge of delivering an incorrect tax return for 2002 had been withdrawn.

At the start of the trial, Mr Lowry (64) of Glenreigh, Holycross, Co Tipperary, pleaded not guilty to all charges. The trial continues.